[Bioperl-l] free software to estimate dS and dN in pairwise comparisons

Fields, Christopher J cjfields at illinois.edu
Wed Jan 11 01:30:52 UTC 2017

I normally would agree, but for anyone working in the commercial domain the licensing is technically and (more importantly) legally ambiguous IMO, and any legal counsel would advise not using the code until that license is clarified one way or another.  This is also the reason Debian won’t release a PAML package it until the language in the README.txt is changed to clarify the license.  

Note (in that thread) this has been going on over a year; the intent is obvious that this should be GPL’d.


On 1/10/17, 5:05 PM, "Horacio Montenegro" <h.montenegro at gmail.com> wrote:

>     ok, I understand now. Anyway, here is a snippet from pamlDOC.pdf
>from PAML 4.9c, reiterating PAML is distributed under GNU GPL license:
>© Copyright 1993-2016 by Ziheng Yang
>The software package is provided "as is" without warranty of any kind.
>In no event shall the author or his employer be held responsible for
>any damage resulting from the use of this software, including but not
>limited to the frustration that you may experience in using the
>package. The program package, including source codes, example data
>sets, executables, and this documentation, is maintained by Ziheng
>Yang and distributed under the GNU GPL v3.
>    The author may have changed his mind, but as far as I can see it
>is still GPLed.
>On Tue, Jan 10, 2017 at 8:32 PM, Fields, Christopher J
><cjfields at illinois.edu> wrote:
>> This is based on the text from the README.txt file with the distribution, which contradicts the license in the ‘src’ directory:
>> ‘PAML is distributed free of charge for academic use only’
>> There are others expressing licensing concerns as well, note this thread from the Debian folks: https://groups.google.com/d/msg/pamlsoftware/NFu_lNBoAEA/VonOWvh6CgAJ
>> BioPerl will always be open and free; Carnë knows this though, he’s a bioperl contributor (and I would consider him a core developer).
>> chris
>> On 1/10/17, 2:38 PM, "Bioperl-l on behalf of Horacio Montenegro" <bioperl-l-bounces+cjfields=illinois.edu at mailman.open-bio.org on behalf of h.montenegro at gmail.com> wrote:
>>     What is free for academic use only? PAML is distributed under GNU GPL
>>     v3 (see "introduction" at [1]), so not restricted to academic use. And
>>     BioPerl is distributed under a dual-license GNU / Artistic License
>>     (see "license" at [2]).
>>     best, Horacio
>>     [1] http://abacus.gene.ucl.ac.uk/software/paml.html
>>     [2] http://search.cpan.org/~cjfields/BioPerl-Run-1.007001/
>>     On Tue, Jan 10, 2017 at 6:19 PM, Carnë Draug <carandraug+dev at gmail.com> wrote:
>>     > I am looking for a piece of free software to estimate synonymous and
>>     > non-synonymous (dS and dN) distances between aligned sequences.
>>     >
>>     > I have found codeml on Bio::Tools::Run::Phylo::PAML::Codeml but that
>>     > is not free software (it's for academic use only).  Can anyone suggest
>>     > an alternative?
>>     >
>>     > Thank you
>>     > Carnë
>>     >
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